Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

T. Z. DeSantis; P. Hugenholtz; N. Larsen; M. Rojas; E. L. Brodie; K. Keller; T. Huber; D. Dalevi; P. Hu; G. L. Andersen

doi:10.1128/AEM.03006-05

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

8821 Citations (Scopus)

Abstract

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Original language	English
Pages (from-to)	5069-5072
Number of pages	4
Journal	Applied and Environmental Microbiology
Volume	72
Issue number	7
DOIs	https://doi.org/10.1128/AEM.03006-05
Publication status	Published - Jul 2006
Externally published	Yes

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AU - DeSantis, T. Z.

AU - Hugenholtz, P.

AU - Larsen, N.

AU - Rojas, M.

AU - Brodie, E. L.

AU - Keller, K.

AU - Huber, T.

AU - Dalevi, D.

AU - Hu, P.

AU - Andersen, G. L.

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AB - A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

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Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

Abstract

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